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An appropriate lipid template structure is selected from a pre-defined list of templates for the specified lipid abbreviation.
The sequence identity of T. curvata polyester hydrolases with the corresponding template structure is summarized in Table 1 and Additional file 1: Figure S1.
In this section, only the general template structure is explained, leaving the description of some specific attribute values to the next sections.
Remarkably, backbone flexibility predicted by FIRST with suitable E c, applied to a single constraint topology (i.e. derived from the native state template structure), is usually similar to the result from the DCM [21].
When three DNA strands with Au nanoparticles are hybridized with each other, a triangular DNA template structure is automatically formed, and then three Au nanoparticles are assembled into a trimer ring structure with nanometer scale gaps.
The incorporation of the two new terms is intended to capture the local structure stiffness when the template structure is aligned with the query sequence.
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Ligand molecular superimposition on the template structure was performed by database alignment method.
Molecular superimposition of antagonists on the template structure was performed by database alignment method.
The ligand molecular superimposition on template structure was performed by atom/shape-based RMS fit, multifit, and RMSD fit methods.
Gaps of missing residues in the loops of the template structure were closed by the 'Loop Search' tool implemented in Sybyl 8.1 (Tripos Inc., St .Louis, Missouri, 63144, USA).
The HDAC1 template structure was obtained from the protein data bank (ID: 4BXK).
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